Abstract
Long non-coding HOX transcript antisense intergenic RNA (HOTAIR) plays an important role in breast cancer. The purpose of this study was to determine whether circulating HOTAIR can be used for breast cancer diagnosis. HOTAIR in serum was measured by PCR-based direct detection. Reverse transcriptase and DNase I treatment were used to distinguish the DNA and RNA forms of HOTAIR. To determine whether circulating HOTAIR is a biomarker for breast cancer, the DNA of HOTAIR from breast cancer patients and healthy controls was measured at both the discovery stage (48 individuals) and an independent validation stage (156 individuals). The diagnostic accuracy was assessed by the receiver operating characteristic curve (ROC) and the area under the curve (AUC). We showed that the major form of HOTAIR-derived fragment in serum is DNA rather than RNA in our study, the same as for MALAT-1, another well-described lincRNA. A higher circulating DNA level of HOTAIR was found in patients at the discovery stage (P = 0.0008). ROC analysis revealed that the circulating HOTAIR DNA distinguished breast cancer patients from healthy individuals (AUC = 0.799). This finding was confirmed at the validation stage. Though circulating MALAT-1 DNA was altered in the discovery stage, it showed no significant difference in the validation stage. In the entire set of 204 samples, the circulating HOTAIR DNA showed a 2.15-fold change in patients compared with healthy controls (P < 0.0001, AUC = 0.786). The optimal cutoff value for diagnosis was 0.30 with sensitivity of 80.0 % and specificity of 68.3 %. Moreover, a correlation between the DNA level of circulating HOTAIR and the progress of breast cancer was established. We have demonstrated that the circulating DNA of HOTAIR is a potential biomarker for breast cancer.
Abbreviations
- AUC:
-
Area under curve
- ER:
-
Estrogen receptor
- HER2:
-
Human epidermal factor 2
- HOTAIR:
-
HOX transcript antisense intergenic RNA
- LN:
-
Lymph node
- LncRNA:
-
Long non-coding RNA
- PR:
-
Progesterone receptor
- ROC:
-
Receiver operating characteristic
References
Thurman RE, Rynes E, Humbert R et al (2012) The accessible chromatin landscape of the human genome. Nature 489(7414):75–82
Djebali S, Davis CA, Merkel A et al (2012) Landscape of transcription in human cells. Nature 489(7414):101–108
Wang H, Maurano MT, Qu H et al (2012) Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res 22(9):1680–1688
Gibb EA, Brown CJ, Lam WL (2011) The functional role of long non-coding RNA in human carcinomas. Mol Cancer 10(1):38
Spizzo R, Almeida MI, Colombatti A et al (2012) Long non-coding RNAs and cancer: a new frontier of translational research? Oncogene 31(43):4577–4587
Reis EM, Verjovski-Almeida S (2012) Perspectives of long non-coding RNAs in cancer diagnostics. Front Genet 3:32
Jemal A, Bray F, Center MM et al (2011) Global cancer statistics. CA Cancer J Clin 61(2):69–90
Bertos NR, Park M (2011) Breast cancer—one term, many entities? J Clin Invest 121(10):3789–3796
Maxmen A (2012) The hard facts. Nature 485(7400):S50–S51
Harris L, Fritsche H, Mennel R et al (2007) American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer. J Clin Oncol 25(33):5287–5312
Duffy MJ, Evoy D, McDermott EW (2010) CA 15-3: uses and limitation as a biomarker for breast cancer. Clin Chim Acta 411(23–24):1869–1874
Patani N, Martin LA, Dowsett M (2013) Biomarkers for the clinical management of breast cancer: international perspective. Int J Cancer 133(1):1–13
Schwarzenbach H, Hoon DS, Pantel K (2011) Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 11(6):426–437
Crowley E, Di Nicolantonio F, Loupakis F et al (2013) Liquid biopsy: monitoring cancer-genetics in the blood. Nat Rev Clin Oncol 10(8):472–484
Umetani N, Giuliano AE, Hiramatsu SH et al (2006) Prediction of breast tumor progression by integrity of free circulating DNA in serum. J Clin Oncol 24(26):4270–4276
Madhavan D, Wallwiener M, Bents K et al (2014) Plasma DNA integrity as a biomarker for primary and metastatic breast cancer and potential marker for early diagnosis. Breast Cancer Res Treat 146(1):163–174
Tangkijvanich P, Hourpai N, Rattanatanyong P et al (2007) Serum LINE-1 hypomethylation as a potential prognostic marker for hepatocellular carcinoma. Clin Chim Acta 379(1–2):127–133
Ren S, Wang F, Shen J et al (2013) Long non-coding RNA metastasis associated in lung adenocarcinoma transcript 1 derived miniRNA as a novel plasma-based biomarker for diagnosing prostate cancer. Eur J Cancer 49(13):2949–2959
Tinzl M, Marberger M, Horvath S et al (2004) DD3PCA3 RNA analysis in urine–a new perspective for detecting prostate cancer. Eur Urol 46(2):182–186
Kumarswamy R, Bauters C, Volkmann I et al (2014) The circulating long non-coding RNA LIPCAR predicts survival in heart failure patients. Circ Res 114:1569–1575
Koh W, Pan W, Gawad C et al (2014) Noninvasive in vivo monitoring of tissue-specific global gene expression in humans. Proc Natl Acad Sci USA 111(20):7361–7366
Lee GL, Dobi A, Srivastava S (2011) Prostate cancer: diagnostic performance of the PCA3 urine test. Nat Rev Urol 8(3):123–124
Rinn JL, Kertesz M, Wang JK et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311–1323
Gupta RA, Shah N, Wang KC et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464(7291):1071–1076
Chisholm KM, Wan Y, Li R et al (2012) Detection of long non-coding RNA in archival tissue: correlation with polycomb protein expression in primary and metastatic breast carcinoma. PLoS One 7(10):e47998
Sorensen KP, Thomassen M, Tan Q et al (2013) Long non-coding RNA HOTAIR is an independent prognostic marker of metastasis in estrogen receptor-positive primary breast cancer. Breast Cancer Res Treat 142(3):529–536
Umetani N, Kim J, Hiramatsu S et al (2006) Increased integrity of free circulating DNA in sera of patients with colorectal or periampullary cancer: direct quantitative PCR for ALU repeats. Clin Chem 52(6):1062–1069
Iorio MV, Ferracin M, Liu CG et al (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65(16):7065–7070
Cantile M, Cindolo L, Napodano G et al (2003) Hyperexpression of locus C genes in the HOX network is strongly associated in vivo with human bladder transitional cell carcinomas. Oncogene 22(41):6462–6468
Fischer U, Keller A, Leidinger P et al (2008) A different view on DNA amplifications indicates frequent, highly complex, and stable amplicons on 12q13-21 in glioma. Mol Cancer Res 6(4):576–584
Trombetta D, Mertens F, Lonoce A et al (2009) Characterization of a hotspot region on chromosome 12 for amplification in ring chromosomes in atypical lipomatous tumors. Genes Chromosom Cancer 48(11):993–1001
Courjal F, Theillet C (1997) Comparative genomic hybridization analysis of breast tumors with predetermined profiles of DNA amplification. Cancer Res 57(19):4368–4377
Page K, Hava N, Ward B et al (2011) Detection of HER2 amplification in circulating free DNA in patients with breast cancer. Br J Cancer 104(8):1342–1348
Pantel K, Alix-Panabieres C (2013) Real-time liquid biopsy in cancer patients: fact or fiction? Cancer Res 73(21):6384–6388
Dawson SJ, Tsui DW, Murtaza M et al (2013) Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 368(13):1199–1209
Skvortsova TE, Rykova EY, Tamkovich SN et al (2006) Cell-free and cell-bound circulating DNA in breast tumours: DNA quantification and analysis of tumour-related gene methylation. Br J Cancer 94(10):1492–1495
Silva JM, Silva J, Sanchez A et al (2002) Tumor DNA in plasma at diagnosis of breast cancer patients is a valuable predictor of disease-free survival. Clin Cancer Res 8(12):3761–3766
Shaw JA, Page K, Blighe K et al (2012) Genomic analysis of circulating cell-free DNA infers breast cancer dormancy. Genome Res 22(2):220–231
Board RE, Wardley AM, Dixon JM et al (2010) Detection of PIK3CA mutations in circulating free DNA in patients with breast cancer. Breast Cancer Res Treat 120(2):461–467
Mouliere F, Robert B, Arnau Peyrotte E et al (2011) High fragmentation characterizes tumour-derived circulating DNA. PLoS One 6(9):e23418
Schwarzenbach H, Eichelser C, Kropidlowski J et al (2012) Loss of heterozygosity at tumor suppressor genes detectable on fractionated circulating cell-free tumor DNA as indicator of breast cancer progression. Clin Cancer Res 18(20):5719–5730
Mouliere F, El Messaoudi S, Pang D et al (2014) Multi-marker analysis of circulating cell-free DNA toward personalized medicine for colorectal cancer. Mol Oncol 8(5):927–941
Asaga S, Kuo C, Nguyen T et al (2011) Direct serum assay for microRNA-21 concentrations in early and advanced breast cancer. Clin Chem 57(1):84–91
Catarino R, Ferreira MM, Rodrigues H et al (2008) Quantification of free circulating tumor DNA as a diagnostic marker for breast cancer. DNA Cell Biol 27(8):415–421
Rogers JC, Boldt D, Kornfeld S et al (1972) Excretion of deoxyribonucleic acid by lymphocytes stimulated with phytohemagglutinin or antigen. Proc Natl Acad Sci USA 69(7):1685–1689
Stroun M, Maurice P, Vasioukhin V et al (2000) The origin and mechanism of circulating DNA. Ann NY Acad Sci 906:161–168
Chan M, Liaw CS, Ji SM et al (2013) Identification of circulating microRNA signatures for breast cancer detection. Clin Cancer Res 19(16):4477–4487
Kodahl AR, Lyng MB, Binder H et al (2014) Novel circulating microRNA signature as a potential non-invasive multi-marker test in ER-positive early-stage breast cancer: a case control study. Mol Oncol 8(5):874–883
Hu Z, Chen X, Zhao Y et al (2010) Serum microRNA signatures identified in a genome-wide serum microRNA expression profiling predict survival of non-small-cell lung cancer. J Clin Oncol 28(10):1721–1726
Kleivi Sahlberg K, Bottai G, Naume B et al (2015) A serum microRNA signature predicts tumor relapse and survival in triple-negative breast cancer patients. Clin Cancer Res 21(5):1207–1214
Acknowledgments
This study was supported by the National High-Tech R&D Program of China (2012AA022501), the National Natural Science Foundation of China (81170097), and the 985 Project of Peking University. We thank Ting Wang for assistance with our experiments.
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No conflict of interest was disclosed.
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Lei Zhang and Xinyun Song have contributed equally to this work.
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Zhang, L., Song, X., Wang, X. et al. Circulating DNA of HOTAIR in serum is a novel biomarker for breast cancer. Breast Cancer Res Treat 152, 199–208 (2015). https://doi.org/10.1007/s10549-015-3431-2
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DOI: https://doi.org/10.1007/s10549-015-3431-2